Mutagenetix > Incidental Mutation

Incidental Mutation 'R7439:Smc5'

576861

Institutional Source

Beutler Lab

Gene Symbol

Smc5

Ensembl Gene

ENSMUSG00000024943

Gene Name

structural maintenance of chromosomes 5

Synonyms

Smc5l1

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7439 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

23206451-23273897 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 23242700 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 467 (V467A)

Ref Sequence

ENSEMBL: ENSMUSP00000084837 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000087556] [ENSMUST00000223934] [ENSMUST00000226111]

AlphaFold

Q8CG46

Predicted Effect

probably damaging
Transcript: ENSMUST00000087556
AA Change: V467A

PolyPhen 2 Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000084837
Gene: ENSMUSG00000024943
AA Change: V467A

Domain	Start	End	E-Value	Type
Pfam:SMC_N	52	1057	9.2e-19	PFAM
Pfam:AAA_23	55	456	1.2e-9	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000223934
AA Change: V467A

PolyPhen 2 Score 0.933 (Sensitivity: 0.80; Specificity: 0.94)

Predicted Effect

probably benign
Transcript: ENSMUST00000226111
AA Change: V391A

PolyPhen 2 Score 0.054 (Sensitivity: 0.94; Specificity: 0.84)

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Homozygous knockout in embryonic stem cells causes abnormal mitosis, increased apoptosis and a shift from pluripotency to differentiation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9530003J23Rik	G	A	10: 117,238,697		probably benign	Het
Acacb	T	C	5: 114,195,642	V542A	possibly damaging	Het
Adprhl1	C	T	8: 13,223,069	V1230I	probably benign	Het
Agpat1	T	A	17: 34,610,909	Y77N	probably damaging	Het
Apc	T	A	18: 34,312,073	I674K	probably damaging	Het
Arpc5	T	C	1: 152,771,436	S97P	probably damaging	Het
Arrdc5	A	G	17: 56,297,931	F119L	probably benign	Het
Asap1	A	G	15: 64,130,256	V402A	probably damaging	Het
Aspg	T	C	12: 112,124,821	V479A	possibly damaging	Het
B3galnt2	G	A	13: 13,994,485	V368M	probably benign	Het
Bcl3	T	C	7: 19,822,611	T23A	probably benign	Het
Bpifb5	A	G	2: 154,228,933	K215E	possibly damaging	Het
Coa4	T	A	7: 100,539,271	C64S	probably damaging	Het
Dcun1d4	T	C	5: 73,491,536		probably null	Het
Dnaaf5	T	G	5: 139,166,113	C506W	probably damaging	Het
Dock3	A	G	9: 107,023,732	Y345H	probably damaging	Het
Dscaml1	A	G	9: 45,710,326	N1024S	possibly damaging	Het
Dsp	T	C	13: 38,176,502		probably null	Het
Dsp	A	G	13: 38,195,449	T2057A	probably benign	Het
Dync1h1	T	G	12: 110,636,453	L2176R	probably damaging	Het
Eif5b	A	C	1: 38,051,637	D1192A	probably benign	Het
Epn2	A	T	11: 61,546,848		probably benign	Het
Exoc1	T	A	5: 76,545,348	N360K	probably benign	Het
Fam135b	A	T	15: 71,463,680	V555E	probably damaging	Het
Fam208a	T	A	14: 27,471,645	V934E	probably damaging	Het
Fmn1	A	T	2: 113,441,611	Q108L	unknown	Het
Gcc2	A	G	10: 58,256,901	T48A	probably benign	Het
Gm438	T	C	4: 144,777,762	D273G	probably damaging	Het
Gm6619	T	G	6: 131,490,391	I73S	possibly damaging	Het
Gm8267	T	A	14: 44,722,940	D116V	probably damaging	Het
Hapln3	T	A	7: 79,117,269	T341S	probably benign	Het
Lamb3	C	A	1: 193,332,166	D544E	possibly damaging	Het
Lhx5	T	A	5: 120,440,284	S390T	probably benign	Het
Lrrc63	A	G	14: 75,126,257	S145P	possibly damaging	Het
Lrriq1	T	C	10: 103,214,519	M791V	probably benign	Het
Lyg2	A	G	1: 37,911,137	Y37H	possibly damaging	Het
Nrbp1	T	A	5: 31,244,956	M172K	probably damaging	Het
Olfr1044	T	A	2: 86,171,010	D269V	probably damaging	Het
Olfr1261	A	G	2: 89,993,839	I149V	probably benign	Het
Olfr168	T	G	16: 19,530,900	S7R	probably benign	Het
Pcyt2	A	T	11: 120,611,383	Y308N	possibly damaging	Het
Peg10	C	CTCA	6: 4,756,453		probably benign	Het
Phf21b	A	G	15: 84,804,903	S141P	probably damaging	Het
Pigh	G	A	12: 79,089,550	P24S	probably benign	Het
Plekhg3	A	G	12: 76,576,485	D834G	probably damaging	Het
Plekhg5	T	A	4: 152,113,935	V860D	probably benign	Het
Pon1	A	G	6: 5,177,399	I170T	probably damaging	Het
Ptpn9	T	A	9: 57,027,433	Y160*	probably null	Het
Ptprj	T	C	2: 90,449,819	K1045R	possibly damaging	Het
Rilpl2	T	A	5: 124,463,788	H196L	probably benign	Het
Rnf112	C	T	11: 61,451,028	V317I	possibly damaging	Het
Rundc3a	G	T	11: 102,400,046		probably null	Het
Sgsm1	T	C	5: 113,274,321	Y489C	probably damaging	Het
Sis	G	A	3: 72,909,041	H1531Y	possibly damaging	Het
Slc26a9	A	G	1: 131,762,818	Y520C	probably damaging	Het
Spata20	G	A	11: 94,484,041	A245V	probably benign	Het
Steap3	A	C	1: 120,241,518	F350V	probably benign	Het
Sucnr1	A	G	3: 60,086,696	Q215R	probably benign	Het
Supv3l1	G	A	10: 62,430,615	A594V	probably damaging	Het
Swt1	A	T	1: 151,411,064	F226I	probably benign	Het
Taar7f	A	G	10: 24,049,987	T160A	possibly damaging	Het
Tada2a	A	T	11: 84,126,986		probably null	Het
Taok3	C	A	5: 117,250,909	Q460K	probably damaging	Het
Twf2	A	G	9: 106,214,398	E268G	probably damaging	Het
Upf2	A	T	2: 6,018,932	I698F	unknown	Het
Vmn2r35	T	A	7: 7,817,014	N86Y	probably damaging	Het
Vmn2r84	T	C	10: 130,392,113	T85A	possibly damaging	Het
Vps13d	A	G	4: 145,105,856	S2833P		Het
Xrn1	T	C	9: 96,051,629	S1584P	probably benign	Het
Zfp354b	T	C	11: 50,922,397	Y567C	probably damaging	Het
Zfp52	A	T	17: 21,560,870	R327*	probably null	Het

Other mutations in Smc5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00569:Smc5	APN	19	23235965	missense	probably damaging	1.00
IGL01070:Smc5	APN	19	23231601	missense	possibly damaging	0.86
IGL01315:Smc5	APN	19	23231604	missense	probably benign
IGL01879:Smc5	APN	19	23228184	missense	probably damaging	0.97
IGL01902:Smc5	APN	19	23259768	missense	possibly damaging	0.85
IGL02016:Smc5	APN	19	23273712	missense	probably benign	0.00
IGL02186:Smc5	APN	19	23231859	missense	probably damaging	1.00
IGL02383:Smc5	APN	19	23214632	splice site	probably benign
IGL02447:Smc5	APN	19	23257492	missense	probably benign	0.01
IGL02534:Smc5	APN	19	23228172	critical splice donor site	probably null
IGL02834:Smc5	APN	19	23257604	missense	probably benign	0.30
IGL03290:Smc5	APN	19	23273658	missense	probably benign	0.19
R0722:Smc5	UTSW	19	23208927	missense	probably damaging	0.99
R0893:Smc5	UTSW	19	23263653	missense	possibly damaging	0.67
R0970:Smc5	UTSW	19	23238998	missense	probably damaging	1.00
R1281:Smc5	UTSW	19	23235883	missense	probably benign
R1368:Smc5	UTSW	19	23210443	missense	probably damaging	1.00
R2092:Smc5	UTSW	19	23238899	missense	probably benign
R3721:Smc5	UTSW	19	23210492	missense	probably benign	0.21
R4382:Smc5	UTSW	19	23268846	missense	probably benign	0.39
R4735:Smc5	UTSW	19	23242705	missense	probably benign
R4936:Smc5	UTSW	19	23234003	missense	probably damaging	1.00
R5306:Smc5	UTSW	19	23259645	critical splice donor site	probably null
R5754:Smc5	UTSW	19	23244103	missense	possibly damaging	0.92
R6175:Smc5	UTSW	19	23214170	missense	possibly damaging	0.60
R6313:Smc5	UTSW	19	23208948	nonsense	probably null
R6527:Smc5	UTSW	19	23228190	missense	probably benign	0.00
R6611:Smc5	UTSW	19	23228919	missense	probably benign	0.13
R6750:Smc5	UTSW	19	23242640	missense	probably damaging	1.00
R6801:Smc5	UTSW	19	23214646	missense	probably benign	0.34
R6821:Smc5	UTSW	19	23242787	missense	probably benign	0.20
R7002:Smc5	UTSW	19	23231883	missense	probably benign	0.00
R7198:Smc5	UTSW	19	23259700	nonsense	probably null
R7386:Smc5	UTSW	19	23215175	missense	possibly damaging	0.59
R7596:Smc5	UTSW	19	23214169	missense	probably damaging	0.99
R7666:Smc5	UTSW	19	23229017	missense	probably benign	0.15
R7760:Smc5	UTSW	19	23235890	missense	probably benign	0.01
R7990:Smc5	UTSW	19	23235882	missense	probably benign	0.01
R8255:Smc5	UTSW	19	23208926	missense
R8359:Smc5	UTSW	19	23234079	missense	possibly damaging	0.49
R8473:Smc5	UTSW	19	23244082	missense	probably benign	0.02
R8711:Smc5	UTSW	19	23265694	missense	probably damaging	0.98
R8815:Smc5	UTSW	19	23244058	missense	probably damaging	1.00
R8885:Smc5	UTSW	19	23213870	missense	probably damaging	0.99
R8940:Smc5	UTSW	19	23259762	missense	probably benign	0.00
R9642:Smc5	UTSW	19	23261388	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- AGCCTCATGGTGATTACAAAGC -3'
(R):5'- GAAGAAACCTGTCATGCCCC -3'

Sequencing Primer
(F):5'- TGGTGATTACAAAGCCAACAAACAG -3'
(R):5'- CTGGAACTCACTTTGTAGACCAGG -3'

Posted On

2019-10-07